/* 
* Copyright (c) 2009, The University of Texas at Austin
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, 
* are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, 
* this list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above copyright notice, 
* this list of conditions and the following disclaimer in the documentation and/or other materials 
* provided with the distribution.
*
* Neither the name of The University of Texas at Austin nor the names of its contributors may be 
* used to endorse or promote products derived from this software without specific prior written 
* permission.
* 
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR 
* IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND 
* FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS 
* BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
* PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF 
* THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/

#pragma once

using namespace System;
using namespace System::Collections::Generic;
using namespace System::Xml::Linq;
#include "RNA.h"

namespace ManagedLabelRNA 
{
	public ref class ManagedRNA
	{
	public:
		ManagedRNA(Dictionary<int,int>^ pairs, int sequenceLength);
		ManagedRNA(const ManagedRNA^ me);
		~ManagedRNA() { delete pUnmanagedRNA; }
		Dictionary<String^, String^>^ ComputeTiered();
		XElement^ ComputeTieredAsXML();
		
	protected:
		String^ ConvertTypeToString(RNA::Label::Type type);
		Dictionary<String^, String^>^ GetStructureElements();
		XElement^ GetStructureElementsXML();
		!ManagedRNA() { delete pUnmanagedRNA; }

	private:
		RNA* pUnmanagedRNA;
	};
}
